18S rRNA amplicon sequencing of seawater and marine sediments in 2018 in Mali Ston Bay aquaculture site

The Adriatic coastal area, where most aquaculture activities are carried out, is often under various anthropogenic influences. Throughout 2018, in Mali Ston Bay, where bivalve and cage fish farms are located, seasonal sampling of seawater and sediment was performed in the scope of selected commercial cage European sea bass farm. The aim of this study was to detect potential pathogenic bacteria and harmful bloom producing algae (HABs), by using high-throughput metabarcoding methods. Physico-chemical parameters were measured in situ, while concentrations of chlorophyll a, total nitrogen and phosphorus were measured in the laboratory. Total DNA was extracted from the samples, and 18S rRNA high-throughput sequencing was performed. Bioinformatics and statistical analysis were performed in QIIME2 and RStudio. Seawater harboured a significant percentage of Dinoflagellata (40.99-67.14%), and sediment Bacillariophyta (32.24-62.25%). Potential HABs of genera Alexandrium, Gonyaulax, Gymnodinium, Heterocapsa were detected in seawater and sediment. Genera Amphidinium and Nitzschia were predominantly found in the sediment, while genera Takayama, Chrysochromulina and Pseudo-nitzschia in seawater. Detection of these taxa coupled with monitoring of environmental parameters, could serve as important biomarkers for aquaculture management and an early warning of health status, protecting both farmed animals and human consumers.